X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedordervector.h;h=7d383ac84f431830e2324cd51d4777d80a3390e0;hp=ef9d6a75b9821ff013a7e94d0c3f67f57886bcf8;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/sharedordervector.h b/sharedordervector.h
index ef9d6a7..7d383ac 100644
--- a/sharedordervector.h
+++ b/sharedordervector.h
@@ -2,25 +2,48 @@
 #define SHAREDORDER_H
 /*
  *  sharedorder.h
- *  Dotur
+ *  Mothur
  *
  *  Created by Sarah Westcott on 12/9/08.
- *  Copyright 2008 __MyCompanyName__. All rights reserved.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
+ 
+ /* This class is a child to datavector.  It represents OTU information at a certain distance. 
+	It is similiar to an order vector except each member of data knows which group it belongs to.
+	Each member of the internal container "data" represents is an individual which knows the OTU from which it came, 
+	the group it is in and the abundance is equal to the OTU number.  */
+
 
-#include <Carbon/Carbon.h>
 #include "datavector.hpp"
-#include "sabundvector.hpp"
-#include "rabundvector.hpp"
 
 struct individual {
 		string group;
 		int bin;
 		int abundance;
+		bool operator()(const individual& i1, const individual& i2) {
+		return (i1.abundance > i2.abundance);
+		}
+	individual() {  group = ""; bin = 0; abundance = 0; }
+};
+
+struct individualFloat {
+		string group;
+		int bin;
+		float abundance;
+		bool operator()(const individual& i1, const individual& i2) {
+		return (i1.abundance > i2.abundance);
+		}
+	individualFloat() { group = ""; bin = 0; abundance = 0.0; }
 };
 
 
+#include "sabundvector.hpp"
+#include "rabundvector.hpp"
+#include "sharedrabundvector.h"
+#include "sharedsabundvector.h"
+#include "groupmap.h"
+
 class SharedOrderVector : public DataVector {
 	
 public:
@@ -29,18 +52,19 @@ public:
 	SharedOrderVector(const SharedOrderVector& ov)	: DataVector(ov.label), data(ov.data), maxRank(ov.maxRank), numBins(ov.numBins), numSeqs(ov.numSeqs), needToUpdate(ov.needToUpdate) {if(needToUpdate == 1){	updateStats();}};
 
 	SharedOrderVector(string, vector<individual>);
-//	SharedOrderVector(ifstream&);
+	SharedOrderVector(ifstream&);
 	~SharedOrderVector(){};
 	
-	void set(int, int, int, string);
+	
 	individual get(int);
-	void push_back(int, int, string);
 	void resize(int);
 	int size();
 	void print(ostream&);
 	vector<individual>::iterator begin();
 	vector<individual>::iterator end();
-
+	void push_back(int, int, string);  //OTU, abundance, group  MUST CALL UPDATE STATS AFTER PUSHBACK!!!
+	void updateStats();
+	void clear();
 
 	int getNumBins();
 	int getNumSeqs();
@@ -50,15 +74,20 @@ public:
 	SAbundVector getSAbundVector();
 	OrderVector getOrderVector(map<string,int>*);
 	SharedOrderVector getSharedOrderVector();
+	SharedRAbundVector getSharedRAbundVector(string);  //get the sharedRabundvector for a sepecific group
+	SharedSAbundVector getSharedSAbundVector(string);	//get the sharedSabundvector for a sepecific group
+	vector<SharedRAbundVector*> getSharedRAbundVector(); //returns sharedRabundVectors for all the users groups
 	
 private:
+	GroupMap* groupmap;
 	vector<individual>  data; 
 	map< int, vector<individual> >::iterator it;
 	int maxRank;
 	int numBins;
 	int numSeqs;
 	bool needToUpdate;
-	void updateStats();
+	void set(int, int, int, string);	//index, OTU, abundance, group
+	
 };
 
 #endif